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1 ---
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2 title: 'FASTA splitter'
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3 output:
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4 html_document:
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5 highlight: pygments
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6 ---
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7
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8 ```{r setup, include=FALSE, warning=FALSE, message=FALSE}
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9 knitr::opts_chunk$set(echo = TRUE, error = TRUE)
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10 ```
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11
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12
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13 ```{bash}
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14 # build job-script
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15 mkdir -p ${WORKING_DIR}/fasta_files
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16
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17 # single-end.sh
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18 cat <<EOF >${X_d}/job-script.sh
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19 ${X_t}/split_multifasta.pl \\
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20 --input_file=${X_A} \\
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21 --seqs_per_file=${X_B} \\
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22 --output_dir=${WORKING_DIR}/fasta_files > ${X_d}/fasta_splitter-log.txt 2>&1
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23 EOF
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24 ```
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25
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26 ```{bash, 'run jobs', echo=FALSE}
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27 # run job script, always use absolute path.
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28 # we want to run all jobs within the working path.
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29 sh ${X_d}/job-script.sh
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30 ```
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31
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32 ```{r, 'display output directory contents', results='asis', echo=FALSE}
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33 ## after the job is done, we list all files from the output directory.
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34 ## full relative path to the output directory needs to be displayed.
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35
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36 cat('##All output files')
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37 cat('\n\n')
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38 all_files = list.files(path = opt$X_d,
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39 full.names = TRUE,
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40 recursive = TRUE)
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41
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42 for (f in sub(opt$X_d, '.', all_files) ) {
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43 cat('* [', f, '](', f, ')\n')
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44 }
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45 cat('\n')
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46 ```
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47
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